ALU TRANSCRIPTS - CYTOPLASMIC LOCALIZATION AND REGULATION BY DNA METHYLATION

Full length Alu transcripts in HeLa cells are detected by primer exten sion using reverse transcriptase and are also analyzed as cloned cDNA sequences. The 5' end of these transcripts corresponds to the transcri ptional start site for RNA polymerase III indicating that these RNAs a re transcribed from their internal polymerase III promoters. The Alu t ranscripts found in cytoplasmic poly A+ RNAs appear to be organized in to RNPs as assayed by sucrose gradient sedimentation. Present at about one hundred to one thousand copies per cell, the Alu transcripts are rare as compared to 7SL RNA. In agreement with previous reports that m ethylation inhibits Pol III-directed transcription of Alu in vitro, tr eatment of HeLa cells with 5-azacytidine results in Alu DNA hypomethyl ation and an increase in the abundance of the Alu transcript. Sequence analysis shows that many different Alu repeats including members of a ll subfamilies are transcribed by Pol III in vivo. cDNA sequences of t he Pol III-directed transcripts exactly match the A box of the Pol III promoter element whereas in other Alu transcripts this element is not faithfully conserved.